Stochastic Modeling of Adaptive Trait Evolution in Phylogenetics: A Polynomial Regression and Approximate Bayesian Computation Approach by Dwueng-Chwuan Jhwueng, Chia-Hua Chang

“…This approach seeks to capture intricate patterns in trait evolution by considering them as continuous stochastic variables along a phylogenetic tree. Using polynomial functions, the model offers a holistic and comprehensive description of the traits of the studied species, accounting for both decreasing and increasing trends over evolutionary time. …”
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Exploring anticancer, antioxidant, and antimicrobial potential of Aspergillus flavus, a fungal endophyte isolated from Dillenia indica leaf callus by Ashish Gupta, Brajesh Chandra Pandey, Mohd Yaseen, Renu Kushwaha, Madhavenda Shukla, Pratima Chaudhary, Partha Pratim Manna, Aparna Singh, Ida Tiwari, Gopal Nath, Nishi Kumari

“…Previously deposited sequences in the Gene bank were used for the identification and making of phylogenetic tree. Antioxidant, antibacterial and anticancer potential of fungal extracts were studied. …”
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Evaluating cutinase from Fusarium oxysporum as a biocatalyst for the degradation of nine synthetic polymer by Maycon Vinicius Damasceno de Oliveira, Gabriel Calandrini, Clauber Henrique Souza da Costa, Carlos Gabriel da Silva de Souza, Cláudio Nahum Alves, José Rogério A. Silva, Anderson H. Lima, Jerônimo Lameira

“…Additionally, analysis of the phylogenetic tree of cutinases produced by different organisms demonstrated that even though the organisms belong to different kingdoms, the cutinase from F. oxysporum (FoCut) showed biological similarity in its activity in degrading polymers with the cutinase enzyme from the bacterium Kineococcus radiotolerans and the fungus Moniliophthora roreri. …”
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Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae by Qian Qin, Yanjing Dong, Jialong Chen, Bo Wang, Yuxin Peng, XinPeng Zhang, Xiaoyun Wang, Jinxiang Zeng, Guoyue Zhong, Shouwen Zhang, Xiaolang Du

“…The topological structure of the constructed phylogenetic tree of 85 species was basically consistent with that of Pap.. …”
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The trend of phylogenetic and epitope variations of SARS-CoV-2 Omicron sub-lineages in Iran by Mehdi Shabani, Ahmad Nejati, Jila Yavarian, Jila Yavarian, Kaveh Sadeghi, Sevrin Zadheidar, Akram Sadat Ahmadi, Monire Ghadirali, Arghavan Zebardast, Adel Abedi, Mohammad Hossein Najmi, Nazanin-Zahra Shafiei-Jandaghi, Talat Mokhtari-Azad

“…The present study evaluated and compared these important variations among different Omicron sub-lineages in Iran.MethodologyFrom October 2023 to August 2024, high coverage whole genome sequences of 49 SARS-CoV-2 strains were subjected to phylogenetic analysis and evaluation of B cell, CD4+, and CD8+ T cell epitopes in Iran National Influenza Centre.ResultsThe phylogenetic tree exhibited eight Nextstrain clades (21L, 22F, 23B, 23H, 23D, 24A, 24B, and 24C) in 48 studied strains, and one recombinant strain (XDK.1). …”
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Genome-Wide Comprehensive Identification and In Silico Characterization of Lectin Receptor-Like Kinase Gene Family in Barley (Hordeum vulgare L.) by Fee Faysal Ahmed, Farah Sumaiya Dola, Md Shohel Ul Islam, Fatema Tuz Zohra, Nasrin Akter, Shaikh Mizanur Rahman, Md. Abdur Rauf Sarkar

“…Therefore, in this study, integrated bioinformatics tools were used to identify and characterize the LecRLK gene family in barley. Based on the phylogenetic tree and domain organization, a total of 113 LecRLK genes were identified in the barley genome (referred to as HvlecRLK) corresponding to the LecRLK genes of Arabidopsis thaliana. …”
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Overexpression of <i>AtruLEA1</i> from <i>Acer truncatum</i> Bunge Enhanced <i>Arabidopsis</i> Drought and Salt Tolerance by Improving ROS-Scavenging Capability by Shaofeng Li, Huijing Meng, Yanfei Yang, Jinna Zhao, Yongxiu Xia, Shaoli Wang, Fei Wang, Guangshun Zheng, Jianbo Li

“…<i>AtruLEA1</i> encodes an LEA protein and is located in the nucleus. Phylogenetic tree analysis revealed a recent affinity of the AtruLEA1 protein to AT3G15760.1. …”
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Genome-Wide Characterization and Expression Analysis of the HD-ZIP Gene Family in Response to Salt Stress in Pepper by Zhongrong Zhang, Ranran Zhu, Xuehua Ji, Hui Ji Li, Hui Lv, Hai Ying Zhang

“…The analysis indicated that the introns number of Ca-HD-ZIP varied from 1 to 17; the number of amino acids was between 119 and 841; the theoretical isoelectric point was between 4.54 and 9.85; the molecular weight was between 14.04 and 92.56; most of them were unstable proteins. The phylogenetic tree divided CaHD-ZIP into 4 subfamilies; 40 CaHD-ZIP genes were located on different chromosomes, and all of them contained the motif 1; two pairs of CaHD-ZIP parallel genes of six paralogism genes were fragment duplications which occurred in 58.28~88.24 million years ago. …”
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Biological characterization of novel Escherichia coli O157:H7 phages and their bacteriostatic effects in milk and pork by Qinghai Ren, Qinghai Ren, Qinghai Ren, Zhiwei Wang, Yichen Ge, Yucui Huang, Wei Zhang, Chunxue Liu, Yubao Li, Shengliang Cao

“…Two phages (vB_EcoP_SD2, vB_EcoP_SD6) of E. coli O157:H7 were isolated from slaughterhouse sewage and characterized for morphology, genomic composition, phage phylogenetic tree, optimal multiplicity of infection (MOI), one-step growth curve, thermal and pH stability and antibacterial efficacy. …”
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Molecular characterization of ST15 carbapenem-resistant Klebsiella pneumoniae isolated in a single patient by Yongjin Hu, Rong Tang, Shanshan Jin, Jiahao Guan, Xiaoxiao Meng, Zengpeijie Dan, Ruilan Wang, Hong-Yu Ou, Jian Lu

“…Phylogenetic analysis showed that these 9 strains constituted a distinct branch within the phylogenetic tree. All nine KP strains belonged to the ST15-KL19 clone. …”
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Trichoderma virens XZ11-1 producing siderophores inhibits the infection of Fusarium oxysporum and promotes plant growth in banana plants by Haiyang Cui, Qifeng Cheng, Tao Jing, Yufeng Chen, Xiaojuan Li, Miaoyi Zhang, Dengfeng Qi, Junting Feng, Farinaz Vafadar, Yongzan Wei, Kai Li, Yankun Zhao, Dengbo Zhou, Jianghui Xie

“…By the analysis of physiological and biochemical profiles, construction of phylogenetic tree, and comparative results from the NR database, strain XZ11-1 was identified as Trichoderma virens. …”
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Expression Analysis and SNP Mining of the Parkin Co-Regulated Gene (PACRG) and parkin in Penaeus vannamei Against White Spot Syndrome Virus by Qian XUE, Xupeng LI, Yang LI, Sheng LUAN, Kun LUO, Jie KONG, Qun XING, Xianhong MENG

“…Amino acid sequence alignment and phylogenetic tree analysis showed that the homology of PACRG between P. vannamei and Penaeus japonicus was the highest at 89.70% similarity. …”
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Genome-Wide Analysis, Characterization, and Expression Profile of the Basic Leucine Zipper Transcription Factor Family in Pineapple by Yanhui Liu, Mengnan Chai, Man Zhang, Qing He, Zhenxia Su, S. V. G. N. Priyadarshani, Liping Liu, Guanxi Dong, Yuan Qin

“…According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure and conserved motif analyses showed that bZIP genes within the same subgroup shared similar intron-exon organizations and motif composition. …”
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Genomic and epidemiological analysis of SARS-CoV-2 variants isolated in Guinea: a routine sequencing implementation by Aminata Mbaye, Haby Diallo, Thibaut Armel Cherif Gnimadi, Kadio Jean Jacques Olivier Kadio, Abdoul Karim Soumah, Joel Balle Koivogui, Jean Louis Monemou, Moriba Kowa Povogui, Djiba Kaba, Castro Hounmenou, Laetitia Serrano, Christelle Butel, Nicolas Fernandez Nuñez, Nicole Vidal, Emilande Guichet, Eric Delaporte, Ahidjo Ayouba, Martine Peeters, Abdoulaye Toure, Alpha Kabinet Keita, AFROSCREEN Team

“…All sequences isolated in Guinea and available on GISAID were included in the analysis for phylogenetic tree and phylodynamic determination. Nextstain tools were used for these analyses. …”
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Mangrove plants using deoxyribonucleic acid barcodes for enhancing biodiversity and conservation by M. Basyuni, R. Syahbana, A.B. Rangkuti, N.A. Pradisty, A. Susilowati, L.A.M. Siregar, S.S. Al Mustaniroh, A.A. Aznawi, A. Mubaraq, E.R. Ardli, S.H. Larekeng, V. Leopardas, Y. Isowa, T. Kajita

“…This study aimed to address the lack of reference deoxyribonucleic acid barcodes from mangroves in North Sumatra and Aceh and assess the effectiveness of four deoxyribonucleic acid barcoding methods in terms of primer universality, successful identification rate, barcoding gap and species-tree inference, and then phylogenetic tree construction. METHODS: This study focused on selecting the main regions where mangroves are predominantly distributed in the provinces of North Sumatra and Aceh: Percut Sei Tuan and Deli Serdang mangrove areas, Pulau Sembilan and Lubuk Kertang of Langkat mangrove areas in North Sumatra, and Langsa mangrove areas in Aceh. …”
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Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins by Hao-Bo Guo, Yue Ma, Gerald A. Tuskan, Xiaohan Yang, Hong Guo

“…The phylogenetic trees generated are biologically meaningful, demonstrating that the protein distributions in the LD space may serve as unique phylogenetic signals of the organisms at the proteome level.…”
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Contribution to the Molecular Phylogeny of Anthribidae (Coleoptera: Curculioniodea) Inferred from COI Sequences by Ali Nafiz Ekiz, Polen Döngel

“…According to the phylogenetic trees, Anthribinae + Coraginae members together constitute a monophyletic clade, which makes currently recognized Anthribinae paraphyletic and Coraginae polyphyletic. …”
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When Three Trees Go to War by van Iersel, Leo, Jones, Mark, Weller, Mathias

“…How many reticulations are needed for a phylogenetic network to display a given set of k phylogenetic trees on n leaves? For k = 2, Baroni et al. …”
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Complete Mitochondrial Genome of <i>Niphon spinosus</i> (Perciformes: Niphonidae): Genome Characterization and Phylogenetic Analysis by Maheshkumar Prakash Patil, Jong-Oh Kim, Seung Hyun Yoo, Jiyoung Shin, Ji-Young Yang, Kyunghoi Kim, Gun-Do Kim

“…Furthermore, we reconstructed phylogenetic trees based on the 13 PCGs. The resulting phylogenetic trees showed <i>N. spinosus</i> placing as a separate lineage within the family Niphonidae, its close relationship to <i>Trachinus draco</i> (Trachinidae), and the clustering of major subfamilies like Luciopercinae and Percinae of the Percoidei suborder. …”
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Testing Phylogenetic Placement Accuracy of DNA Barcode Sequences on a Fish Backbone Tree: Implications of Backbone Tree Completeness and Species Representation by M. A. Thanuja M. Fernando, Jinzhong Fu, Sarah J. Adamowicz

“…In conclusion, COI‐based placement analysis represents a potential route of using the available vast barcoding data for building large phylogenetic trees.…”
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